Re: [PyMOL] causing to miss atoms
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Wed, Aug 1, 2018 at 8:29 AM Mohammad Goodarzi wrote: > Hi Kevin, > > Yes I am talking about the the C-terminal Ser in the chain A of 2J3S. How > can I fix that ? I would like to do other work with this chain like > homology modeling, mutation influence on domian etc using Gromacs. but This > Ser in C-terminal has a missing so I cannot do anything about it. > what is your thought? > > Thanks > Mohammad > > > > > > On Wed, Aug 1, 2018 at 10:25 AM Kevin Jude wrote: > >> Please be more specific with your questions. Which atoms? Which Ser? How >> did you remove chain B, etc? >> >> For some reason only the N is modeled for the C-terminal Ser in both >> chains of 2J3S; if that's what you're talking about, then the issue is with >> the deposited PDB file, and likely the atoms were not visible in electron >> density. If you're talking about other Ser residues then you'll have to >> give more information. >> >> Best wishes >> Kevin >> >> -- >> Kevin Jude, PhD >> Structural Biology Research Specialist, Garcia Lab >> Howard Hughes Medical Institute >> Stanford University School of Medicine >> Beckman B177, 279 Campus Drive, Stanford CA 94305 >> Phone: (650) 723-6431 >> >> On Wed, Aug 1, 2018 at 8:03 AM Mohammad Goodarzi < >> mohammad.goda...@gmail.com> wrote: >> >>> Hello, >>> >>> I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S >>> then I try to remove the chain B, and all water etc except the chain A. >>> it causes that I miss some atoms on the SER. Can you please advise how >>> to deal with it? >>> >>> Thanks >>> Mohammad >>> >>> -- >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> ___ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] causing to miss atoms
Hi Kevin, Yes I am talking about the the C-terminal Ser in the chain A of 2J3S. How can I fix that ? I would like to do other work with this chain like homology modeling, mutation influence on domian etc using Gromacs. but This Ser in C-terminal has a missing so I cannot do anything about it. what is your thought? Thanks Mohammad On Wed, Aug 1, 2018 at 10:25 AM Kevin Jude wrote: > Please be more specific with your questions. Which atoms? Which Ser? How > did you remove chain B, etc? > > For some reason only the N is modeled for the C-terminal Ser in both > chains of 2J3S; if that's what you're talking about, then the issue is with > the deposited PDB file, and likely the atoms were not visible in electron > density. If you're talking about other Ser residues then you'll have to > give more information. > > Best wishes > Kevin > > -- > Kevin Jude, PhD > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > On Wed, Aug 1, 2018 at 8:03 AM Mohammad Goodarzi < > mohammad.goda...@gmail.com> wrote: > >> Hello, >> >> I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S >> then I try to remove the chain B, and all water etc except the chain A. >> it causes that I miss some atoms on the SER. Can you please advise how to >> deal with it? >> >> Thanks >> Mohammad >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] causing to miss atoms
Please be more specific with your questions. Which atoms? Which Ser? How did you remove chain B, etc? For some reason only the N is modeled for the C-terminal Ser in both chains of 2J3S; if that's what you're talking about, then the issue is with the deposited PDB file, and likely the atoms were not visible in electron density. If you're talking about other Ser residues then you'll have to give more information. Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Wed, Aug 1, 2018 at 8:03 AM Mohammad Goodarzi wrote: > Hello, > > I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S > then I try to remove the chain B, and all water etc except the chain A. > it causes that I miss some atoms on the SER. Can you please advise how to > deal with it? > > Thanks > Mohammad > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] causing to miss atoms
Hello, I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S then I try to remove the chain B, and all water etc except the chain A. it causes that I miss some atoms on the SER. Can you please advise how to deal with it? Thanks Mohammad -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
